OK, I know the problem.
The line above the Mart is due to the Mountains. They are 1 pixel too low, so they interfere with the Mart and PC.
The Pallet Town problem is something you did. Pallet Town uses a different tileset now, because you accidently edited it. Instead of reinserting Pallet Town's tileset, you must have accidently loaded Viridian's tileset, as all the tiles there are Viridian's now, yet should be Pallet Town's.